Project description:Because the minimal chloroplast genome carries very limited genetic information, plants rely on signals sent from the chloroplasts to the nucleus for proper chloroplast development as well as for recovery from photoinhibition and response to photo-oxidative stress. In this study, we report the discovery of several factors involved in the reduced PQ pool-driven chloroplast-to-nucleus signaling process. High-throughput RNA-Seq expression profiling of tanorexia-1 (tnr-1) mutants in comparison to wild-type. From these experiments, we found out that the HSF and HAC1 transcription factors have broad effects on HL-driven nuclear gene expression. The DEAD-box RNA helicase 38, CRY1 and a previously uncharacterized G-patch domain-containing protein are also involved in the signaling.

2013-10-02 | E-MTAB-4255 | biostudies-arrayexpress

Nuclear gene expression in response to chloroplast division inhibition

Project description:The aim of this investigation is to analyse the effect on nuclear gene expression of inhibition of chloroplast division. Transgenic Arabidopsis lines (Ler) were generated that contained a chemically inducible promoter (XVE) upstream of AtMinD1. AtMinD1 encodes a product involved in chloroplast division; overexpression of AtMinD1 leads to chloroplast division inhibition. 6 samples were used in this experiment. Three treatments were performed: Treatment 1: Empty vector control seedlings (transformed with PER-10 only) were sown onto lehle, sprayed at 13 days old with 2uM 17-B-estradiol (inducer) and harvested 24 hours later. Treatment 2: Seeds were sown on lehle containing inducer and sprayed every 24 hours with 2uM inducer until harvested at 14 days old. Treatment 3: Seeds were sown on lehle plates, sprayed at 13 days old with 2uM inducer and harvested 24 hours later. For all three treatments, seedlings were grown in constant light conditions, and tissue was harvested from 14-day-old seedlings (4 rosette leaves) and snap frozen in liquid nitrogen before RNA preparation.

2010-04-28 | E-GEOD-20228 | biostudies-arrayexpress

Expression data from Arabidopsis thaliana seedlings with reduced synthesis of 5-aminolevulinic acid

Project description:5-aminolevulinic acid (ALA) is the common precursor of all biological synthezised tetrapyrroles. Inhibition of ALA synthesis results in decreased amounts of chlorophylls, heme, siroheme and phytochrome. It was previously shown that 4 out of 5 Arabidopsis mutants uncoupling nuclear gene expression from the physiological state of the chloroplast are affected in plant tetrapyrrole biosynthesis. It is common to all four mutants to show a reduced ALA formation. We investigate the impact of reduced plastidic ALA synthesis on nuclear gene expression by inhibition of ALA formation using gabaculin and compare these effects with the gun4-1 mutant. Formation of 5-aminolevulinic acid was inhibited in Arabidopsis thaliana Col-0 seedlings by application of 10 µM gabaculin. Additionally the Arabidopsis gun4-1 mutant was investigated. Seedlings were etiolated for 3 days on MS medium in absence or presence of gabaculin and subsequently deetiolated for 6 hours. Total RNA was extracted and used for microarray hybridisation.

2011-04-01 | E-GEOD-27704 | biostudies-arrayexpress

EXECUTER1- and EXECUTER2-dependent transfer of stress signals from the plastid to the nucleus of Arabidopsis thaliana

Project description:Shortly after the release of singlet oxygen (1O2), drastic changes in nuclear gene expression occur in the conditional flu mutant of Arabidopsis that reveal a rapid transfer of signals from the plastid to the nucleus. In contrast to retrograde control of nuclear gene expression by plastid signals described earlier, the primary effect of 1O2 generation in the flu mutant is not the control of chloroplast biogenesis but the activation of a broad range of signaling pathways known to be involved in biotic and abiotic stress responses. This activity of a plastid-derived signal suggests a new function of the chloroplast, namely that of a sensor of environmental changes that activates a broad range of stress responses. Inactivation of the plastid protein EXECUTER1 attenuates the extent of 1O2-induced up-regulation of nuclear gene expression, but it does not fully eliminate these changes. A second related nuclear-encoded protein, dubbed EXECUTER2, has been identified that is also implicated with the signaling of 1O2-dependent nuclear gene expression changes. Like EXECUTER1, EXECUTER2 is confined to the plastid. Inactivation of both EXECUTER proteins in the ex1/ex2/flu triple mutant is sufficient to suppress the up-regulation of almost all 1O2-responsive genes. Retrograde control of 1O2-responsive genes requires the concerted action of both EXECUTER proteins within the plastid compartment. Keywords: biotic and abiotic stress response, nuclear gene expression, plastid-derived signal, Col-0 ecotype, continuous light and then dark-incubated plants

2008-02-14 | GSE10509 | GEO

Expression data from early Arabidopsis thaliana embryo

Project description:After zygote division, the resulting daughter cells progressively give rise to two very different tissue types. With the use of microarrays, global nuclear expression profiles were generated.

2014-10-23 | GSE60242 | GEO

ChIP-Seq data from Arabidopsis thaliana under dark and far-red light

Project description:FAR-RED ELONGATED HYPOCOTYL 3 (FHY3) and its homolog FAR-RED IMPAIRED RESPONSE 1 (FAR1) are two transposase-derived transcription factors initially identified as the key components in phytochrome A signaling and recently shown to function in the circadian clock. However, whether FHY3 and FAR1 are involved in other processes of plant development remains largely unknown. Here, we explored chromatin immunoprecipitation-based sequencing (ChIP-seq) analysis to identify 1745 and 1171 FHY3 direct binding target genes in darkness and far-red light conditions, respectively in the Arabidopsis thaliana genome. This analysis revealed that FHY3 preferentially binds to the gene promoters through the previously identified typical FHY3/FAR1 binding motif. Interestingly, FHY3 also binds to two novel motifs in the 178-bp repeats of the Arabidopsis centromere regions in vivo. Comparison between the ChIP-seq and microarray data indicates that FHY3 regulates the expression of 196 and 85 genes in dark and far-red respectively by directly binding to their promoters. FHY3 also co-regulates a number of common target genes with PHYTOCHROME INTERACTING FACTOR 3-LIKE 5 (PIL5) and ELONGATED HYPOCOTYL 5 (HY5). Moreover, our genome-wide identification of FHY3 direct target genes ultimately led to the discovery and validation of a new role of FHY3 in controlling chloroplast development, by directly activating the expression of ACCUMULATION AND REPLICATION OF CHLOROPLASTS5 (ARC5), a key gene regulating chloroplast constriction and division. Taken together, our data suggest that FHY3 is involved in regulating multiple facets of plant development, thus providing new insights into the functions of this type of transposase-derived transcription factors.

2011-08-02 | GSE30711 | GEO

Expression data from Arabidopsis thaliana (Ler) rosette leaves after the release of singlet oxygen inside plastids

Project description:We used the flu mutant of Arabidopsis to detail gene expression in response to singlet oxygen. The conditional flu mutant of Arabidopsis accumulates excess protochlorophyllide in the dark within chloroplast membranes that upon illumination acts as a photosensitizer and generates singlet oxygen. Immediately after the release of singlet oxygen mature flu plants stop growing, whereas seedlings bleach and die. Within the first 30 min after the release of singlet oxygen rapid changes in nuclear gene expression occur. Distinct sets of genes were activated that were different from those induced by other reactive oxygen species, superoxide or hydrogen peroxide. Keywords: Time course

2008-03-18 | GSE10876 | GEO

Expression data from Arabidopsis thaliana under dark and far-red light

2011-08-02 | GSE30712 | GEO